Soul Eater: The Omegian War
by Death Evans 88
Summary: After the first loss serious against Omega's weapon, the team now has to come to grips with this loss, as Omega begins to raise his army. Can Layle and the others come to grip with there loss and move on, or will the war go to Omega. Read to find out.
1. Chapter 1

**Death Evans 88: Hello all my loyal fans and welcome to the next story in the Soul Eater Chaos Saga, SE: The Omegian War.**

**Layle: Yeah this should be fun, oh hey aren't you writing three stories... are you sure you can do that.**

**Death Evans 88: Hell yes I can, now all of your readers sit back and enjoy my second third story on Fan fiction. Oh and remember that one I don't own anything Square Enix and company own, and that at the end of each chapter, REVIEW, come on people, I know one person who reviews constantly and I thank you, Shadowmistx98. Now enjoy. Also thanks to my Editor who will has gotten me off my lazy but. Sorry for the wait enjoy.**

_Chapter One: The Familiar Scene_

_~Alyssa~_

I sat next to a set of white hospital beds, where Soul Eater Evans, a white haired Death scythe, and Layle Muchitsujo, my brown haired Meister and boyfriend, laid, unconscious. Next to Soul's bed was a petite ash blond haired Meister, Maka Albarn, who in addition to being the leader of Spartoi, the elite student organization, and a two star Meister, was the girlfriend of Soul. She was crying, like she had been for the last five days. Every time she saw Soul's dormant form, tears welled up in her green eyes.

"Maka, I think we should get some food and then sleep now." I said this as I got up, seeing that it was already seven at night. I put a hand on her shoulder. She looked up, teary eyed, but sadly nodded and got up. We left the hospital in silence, walking all the way to Layle and my apartment. As soon as we got in, she went into my room and closed the door. I silently counted to ten as I grabbed some leftovers to heat up for dinner. As soon as I reached ten, I heard light sobbing from my room. _'Goddamn It all, Layle or Soul better get better soon or I'm going to have to try cooking, which isn't a good idea.' _I thought this as I cooked the leftovers and looked at what we had left. I had maybe two weeks left, but I was getting tired of leftovers. I thought back on how we got ourselves into this mess.

It was after the horrendous fight against the Omega Weapon Mark I. Maka and I were the only people left conscious from the fight. We were able to get everyone back to Death City, where the other were rushed to the hospital. The next day, Thea, Serenay, Ryo, Nico, Tsubaki, Liz, Patti, Chrona, Kid, and Black*Star were all discharged, each of them only having a broken bone or two.

However, Layle, who I presumed would be more hurt than the others because of his stupid heroics, and Soul were not discharged, due to the fact they both were unconscious. They were stuck in this familiar scene, a scene that I had seen enough times to know that Layle would be alright, but Maka was terrified about Soul. I tried to reassure her that Soul would be alright, but she almost instantly became an emotional wreck. She spent most of the last five days in my room crying.

Maka had also been temporarily relieved of her leadership of Spartoi, and was taken off the roster for mission candidates, like I was. Kid was the temporary leader of Spartoi, though almost none of Spartoi was doing missions.

"Maka, I'm coming in." I said this as I knocked on my door, her dinner in my hand. I heard her stop sobbing, and she opened the door.

"Thanks Alyssa." Maka said this in a weak voice, which was normally unusual for her. She looked like hell, her ash blonde hair in a rats nest, eyes red and puffy as well. She was wearing one of Soul's shirts, a pair of silk pajama pants, and she was holding Soul's old white headband, which he showed Layle once, that was wet with her tears.

"Maka, if you need to talk, I'm here for you." I said this as I walked out to eat my dinner. Maka came out of my room, dropped her dishes in the sink and went back to my room. I sighed as she didn't say a word. After about two hours, I decided to go to bed, so I went into Layle's room, where I had been sleeping for the past five days, and got ready for bed. I had just laid down, when I heard a knock on the door. I groaned and got up and opened the door, standing there was Maka.

"Hey Alyssa, can I talk to you." I nodded, flicking the light on and letting her into the oddly clean room. She went and sat on the bed, and looked at me. "Alyssa, how do you deal with Layle being in the hospital? Aren't you scared at all for him, how you are not fazed by this?" Maka said this, almost screaming. I smiled and sat next to her. I put a hand on her shoulder before I spoke.

"It's quite easy; I know our two idiots are strong enough to pull through this. I mean come on Maka, Soul has nearly been sliced in half, and Layle nearly got stabbed in the heart. Compared to that, a little blast isn't going to keep them down. Plus those two are like Black*Star at times, they just don't know how to give up." I watched Maka's eyes light up as I said this, and she smiled.

"Thanks Alyssa, you're right, that idiot Soul has gone through worse, and still pulled through." She said this in a stronger, more confident voice, with a fire blazing in her eyes. She thanked me again and went to bed, just as I did.

~Maka~

The first thing I heard when I woke up was the phone ringing. Alyssa picked it up as I exited her room. I went to the kitchen to grab something to eat when she started yelling.

"Maka, get dressed, we have to get to the hospital right away." I jumped when Alyssa yelled this, and instantly I thought that something happened to Soul. I instantly ran into Alyssa's room and changed. When I came out Alyssa said we were taking Layle's bike, which was weird. Soon we were driving to the hospital, my stomach tightening, hoping that the worst hadn't happen. Alyssa and I ran too Soul and Layle's room. I ran into the room before Alyssa.

"Hey Maka, please tell me you're here to pick me up." I saw Soul sitting up as he said this and I nearly launched myself onto him. He smirked when Alyssa came in with a sly smile.

"Soul, you're okay." I walked over and hugged him as he got out of his bed, dressed in an orange shirt and black pants. He smiled and ruffled my hair. After talking with the doctor for a bit, we left.

~Alyssa~

I walked home from the Hospital, letting Maka and Soul use the bike. I used this time to think on a million different things, but mainly Layle. I knew that when Layle woke up, he might be different. I sighed as I got near the apartment complex. _'Trust me I won't change.'_ I stopped at the door as I heard this, it sounded like Layle. I sighed and smiled. _'Great, now I'm hearing his voice in my head ah well.'_ I shrugged and walked into the door, barely hearing the next thing.

_"I'm never going to leave you Lyss."_

**Death Evans 88: And there you go, Chapter one is done. Watch for Chapter Two.**

**Layle: Yeah, and DE will try and update as soon as he can, but he is limited on what he can do.**

**Shikyo: Yeah.**

**DE88 & Layle: Where did you come from!**

**Shikyo: I walked in.**

**DE88: Okay then you gets to say the end.**

**Shikyo: Okay, read and Review, or someone will find you.**


	2. Chapter 2

**DE88: DE88 here with a chapter for Soul Eater: The Omegian War.**

**Layle: Damn I thought you forgot about us.**

**DE88: Nope, anyways, here is the chappie, enjoy.**

_~Chapter two: Awakening~_

_~Serenay~_

"Hyahh!" I yelled this as I flashed by a Kishin, causing it to transform into a red, plated soul, which was promptly absorbed into Thea's sheathe, which Sid and Nygus gave to her. "Whew. Hey Thea, how many souls does that make?" I asked my weapon this as I sheathed her in her combat knife form.

"This soul makes ninety six." Thea said this in her metallic weapon voice and I smiled, knowing that we were close to our goal. I sighed and jumped from the roof top we were on, as the Kishin decided to run and be difficult, and called Carbuncle as we fell. As soon as the bike hit the ground, I twisted my wrist forward, making the bike shoot forward and fly down the street. "Ugh, Serenay. Please don't do that again." I giggled slightly as Thea said this in a disgusted voice.

"Don't worry, I won't." I said this as I flew down multiple roads, weaving through cars and trucks on the highway. After a few hours later, we got to Death City, waiting there was a blue hair boy, standing there with his short, black haired weapon partner.

"You're late Serenay." I sighed when my blue haired boyfriend, Ryo said this. He had a smirk on his face, and he was leaning against a wall.

"It doesn't help when I have to chase a Kishin across a whole city." I said this as Thea transformed into her normal red headed human form. She smiled at Nico, her boyfriend. Since they started dating, Thea wore her ninja mask less, probably because she wasn't emotionless all the time, but instead smiling.

"Well that sucks for you, should have caught it sooner, slowpoke." Nico said this in a cocky voice as he walked next to Thea. "So then shall we leave?" Nico asked this, in what he'd call a charming voice, and Thea threw her elbow into his stomach, making him double over in mock pain.

"That was rude. Apologize, and then we shall leave." Thea said this tonelessly, which I knew as her voice that she used when she meant business. Nico gulped and gave a weak apology before leaving with Thea. As they left I started giggling and sighed.

"So what do we do now?" I turned to Ryo as I said this, giving him a huge grin. He merely shrugged and grinned. I sighed and rolled my eyes as I held his hand. "You never plan things out, do you idiot." I said this in a lightly irritated sounding voice. Ryo smirked and kissed me before speaking.

"How about some dinner?" He said this with a smile. I smiled back and nodded, both of us getting on our bikes and driving to Ryo's favorite fast food place. After talking and eating fifteen bucks worth of food, Ryo and I dropped off Carbuncle and Slydra at our apartment building, and walked to Death Robins, which was only half a block away.

"So, how was Layle today?" I asked Ryo this as I licked my rocky road ice cream. I knew that today was his day to check up on Layle and Alyssa, seeing as all of Spartoi unanimously decided we should check up on the two of them. Ryo shrugged and finished his ice cream.

"He seemed the same as ever." Ryo said this in a serious tone of voice and I sighed. Layle had been admitted to the hospital with Soul three months ago. This was a long time to be in there, especially for someone like Layle, who healed fast. I thought about how Soul recovered quickly, and how Layle seemed to always over use his powers. I soon started to stare off into space, thinking of hundreds of possibilities of why Layle was still unconscious. "You want to go see him?" I jumped when Ryo said this. Somehow we were at the garage of the apartments, and my ice cream was gone.

"I don't know…" I said this in a soft, sad voice, and looked down so that Ryo couldn't see the tears forming in my eyes. _'What if he actually dies!? What if he does wake up, and doesn't remember anyone!?' _ I mentally yelled this out, and of course, when I needed some form of answer, Selen was quiet. I closed my eyes as some of my tears escaped from them, and I felt a pair of arms wrap around me. _'Ryo…'_ Was my only thought. I looked up and opened my eyes to see him with a soft, caring look on his face.

"Serenay, it's okay to be afraid and show you emotions. He's your brother, so it's alright to cry for him." Ryo said this softly before kissing me again. _'Ryo is right, you've been so closed off that no one knows how you are feeling, and they want to know.' _ Of course Selen decided to pipe up at this time, just as Ryo broke the kiss. I smiled softly, letting a few more tears escape my eyes.

"You are absolutely right Ryo… Let's go see him." I said this as I stepped out of his grasped and grabbed Carbuncle, tossing him his helmet as I did so. He grinned before putting it on and getting on the back of my bike, which I instantly willed to life and roared down the street to the hospital. After we got there, we instantly headed to Layle's room, showing the nurse our DWMA Meister badges. As we got near the room, Alyssa burst out of it, and ran straight into me, knocking me down and causing her to fall on top of me.

"Oh Death, I'm so sorry Serenay." Alyssa said this as she bounced right up, huge grin plastered on her face. She held out a hand to help me up, which I accepted. Ryo was on the side, chuckling.

"It's no problem, but what's the hurry?" I asked this as I brushed myself off. Alyssa merely giggled and started moving past me.

"Go see for yourself, I have to get home." Alyssa said this as she ran out of the hospital faster than if someone shot her out of a cannon, or if Stein was chasing her with a scalpel. Ryo and I shared a quick glance as my heart soared. We both thought of the same thing, and proceed to the door Alyssa had ran out of. I of course went in first.

"Wow, the second person here is my little sister and her boyfriend, like I didn't see that one coming." Inside was Layle, who had a grin on his face and was dressed in white hospital pajamas. He was sitting on the side of the bed. I instantly did something that not everyone would expect. I tackled Layle into a hug.

"Layle, you're finally awake!" I yelled this as I hugged him. He started laughing and I looked up to see his signature smile, which caused me to grin. I soon let go of him and Ryo playfully muttered something about wanting the same reaction.

"Yeah I am. Now I just have to wait for Alyssa to get back with my clothes." Layle said this as he stretched and smiled. Even with how fast Alyssa ran, Ryo and I still had and entire hour to tell Layle everything that had gone on while he was out cold.

**DE88: Finally it is done.**

**Layle: Yep, now to just write the rest. Remember folks, READ AND REVIEW. OR NO COOKIES FOR YOU.**


	3. Chapter 3

**DE88: Hiya, I'm back with a new chapter. If you like my story, follow me and check out my bleach and KH stories. So enjoy this next chapter, and remember to review.**

_~Chapter Three: Secrets and Lies~_

_~Layle~_

Life seemed to return to normal after I got released from the hospital. Everyone in Spartoi, and the whole EAT class was overjoyed to see me. Even Stein looked happy to see me, though I don't know if it was me, or his recent wedding, or just the fact that he wanted to dissect me….I personally hoped it was the first two. The person who was the happiest in all of Death City was Alyssa. She basically had a smile super glued onto her face. Nothing could dampen her mood, and life seemed great. But something felt off to me.

A week after I got out of the hospital I was sitting on the living room couch, reading a book while one of the music channels was playing. It was after dinner and it was Alyssa's turn to clean the kitchen.

"Hey Layle, you got a letter." I looked up from my book when Alyssa said this, walking out of the kitchen with a milky white envelope in hand.

"Really? Who in the world would send me a bloody letter instead of a bloody text message?" I said this as I accepted the letter from Alyssa, and she started laughing.

"Wow, you and England really don't mix well." Alyssa said this teasingly, causing me to laugh. We had come back from a mission in England two days ago. Evidently the time we stayed there was long enough for me to get a slight accent. I smiled and turned the letter over when Alyssa left the room, and saw that the letter had no return address, and that the handwriting for the address was all too familiar. _'Wait a minute…Layle isn't that…' _I physically and mentally nodded to Chaos as he said this, checking that Alyssa was busy. _'There is no doubt; it is Carmine's hand writing.'_ I mentally said this to Chaos as I opened the letter to read it

'Dear Layle,

I hope you like how I sent this letter. I made sure that your little girlfriend couldn't tell it was me. I want you to come to the place where it all began for you, and where it ended for me. Come alone. If anyone follows you, I will kill them.

Your Ex-Partner,

Carmine'

I instantly tore the paper to shreds and threw it away. _'You know she means business.' _ I sighed when Chaos said this as I picked my book to continue reading. _'Yeah I know…and I know what I have to do.'_ I said this to Chaos as Alyssa entered the room and sat next to me.

"You alright Lay?" I looked up when Alyssa said this and smiled.

"Yeah, I'm fine." I said this in a cheer tone that was completely opposite from what I felt. I was lucky that Chaos was blocking the connection between Alyssa and me, or else Alyssa would know I was lying. Alyssa looked at me with a weird look that told me she suspected something, but she merely shrugged.

"Okay, what happen to the letter?" I nearly stiffened up as she said this innocently, but I managed to keep my reaction in my head and I chuckled a bit.

"It was some junk mail, probably from Nico or Black*Star, so I tore it up and threw it away." I said this jokingly, even though I was lying through my teeth. Alyssa started giggling, which soon led to her laughing and caused me to laugh. The two of us then talked for hours, till Alyssa got tired and went to sleep early. I stayed in the living room till I was absolutely sure that she was asleep, which was about thirty minutes later.

"Sorry Lyss, but I need to do this a certain way." I whispered this to myself as I got up and wrote a note for Alyssa, and put it on the fridge before I silently crept out of the apartment building and started walking towards the entrance of Death City, calling Diablos as I got near.

~Alyssa~

I woke up late in the morning to a strange silence in the apartment, which made everything seem off. For one I should either hear music, or Layle's snoring, and I heard nothing, not even the shower running. I quickly got dressed and searched our apartment, not finding him. I was about to try and call his phone when I saw a note on the fridge. I instantly snatched it up.

'Lyss,

I'm sorry for leaving without telling you. The letter I got yesterday was from Carmine, not Nico or Black*Star. I'm terribly sorry for lying to you, but this had to be done this way. Do not come looking after me, no matter what. I'll have Serenay come over, please show her this letter, she will understand.

Love,

Layle

P.S. The place where our journey began.'

I let the note slip out of my hands as I finished reading it. I stood there, realizing that I wasn't imagining that Layle looked distracted last night, and that he was going straight into a trap most likely. He lied to me, only so he could protect me. I probably would have stayed in shock for a while, if someone hadn't knocked on my door.

"Yes who is it?" I said this in a dazed tone as I opened the door to reveal Serenay standing at my door way with Thea.

"Alyssa are you alright?" Serenay asked this in a concerned voice as they followed me into the kitchen. "Layle said that I needed to talk to you for some reason." I nodded as I picked up the note, unable to speak. I wordlessly put it into her hand. She quickly scanned it, and smiled when she did. "So Layle is heading home, and he wants us to follow. Nice thinking on his part." I looked at her when she said this and she grinned.

"But it says not to follow him." I said this in a sad tone, but Thea just simply put a hand on my shoulder.

"The thing is with Layle's notes; you never listen to anything underlined. It's a kind of simple code that he came up with for these kinds of situations." Thea said this sweetly as Serenay tossed me some keys. I caught them deftly and stood there for a second before putting on a wicked smile. I followed Serenay down stairs and got on Carbuncle, and went after Layle.

**DE88: So there is Chappy 3, now review, or no cookies.**


	4. Chapter 4

**DE88: Hey people of the internet, it's me Death, I'm here again with another chapter of SE: the Omegian War. Now just as a warning, starting from this chapter and onwards, you may get a wee bit confused about everything if you haven't read SE: New Beginnings; The Rise of Madness and Chaos, or The Truth of the Last Name. Enjoy.**

_Chapter Four: Survivor_

_~Layle~_

I stopped Diablos when we reached the outskirts of the ruined town. It seemed that even though three years had passed, this place still gave me the chills. I kicked the kickstand out for Diablos and got off. I walked to what use to be the town square, the place where my friends and I would play, but now it was a grave yard. I calmly walked through the rows of graves, finding one of the few white marble gravestones in the middle of the graveyard. I bent down and read the inscription that I had carved so long ago.

'Here lies Lenora Renay Sotamora, a loving mother. May she rest in peace.'

I felt tears form in my eyes as I read the simple line, and I didn't care. I reached my hand out and touched the grave, tears silently falling down my face.

"Hey mom….sorry I haven't been by in three years. Things have become complicated. Serenay, Thea, and are fine….but we all miss you…." I whispered this, and soon found I couldn't say anything else. I stayed there, thankful that Chaos was quite, till I sighed and wiped my eyes. I got up and began to walk towards two souls that were at the other end of the town.

"Glad you could make it Layle." Carmine said this as I walked up to her and Zane. She jumped down from a broken wall she was sitting on, and landed next to a motionless Zane, which though the guy was quite, he looked like a zombie, not even looking at me…just a blank stare.

"As much as I'd like to know why you picked here of all places, I think it's better that we cut to the chase, Carmine. Now what do you want." I said this with a bit of malice in my voice. She smiled and tossed me a flask, which I caught easily. Inside was an Akuma-Kon soul. "What the hell." I looked at soul, surprised.

"That is the soul of Shikyo, Akuma-Kon of darkness. Think of it as a peace offering." Carmine said this in surprisingly truthful voice. I shrugged and summoned Diablos, putting the soul in the saddle bags for later before I dismissed the bike. "Now then, Omega has a gracious offer for you." I looked at Carmine with a bored look on my face.

"What is it, and if I don't like it you know it's a no." Carmine looked smug as I said this coldly. She had the face of someone who had just won. She held out a gold armlet with the symbol of Omega engraved in it.

"Join Omega, and he will give you the last two Akuma-Kon souls, and Chaos will be his right hand man once more. And as a bonus, your little girlfriend gets her brother back." She said this as she pointed her thumb at the unresponsive Zane. I froze as she said this though. Not only was Omega giving me the power to beat him, but also Zane…I won't say I wasn't tempted, hell even Chaos was contemplating the idea of changing sides.

"You think I'm just going to turn on everyone I care about." I said this in a low voice. Carmine simply smiled and giggled.

"Yeah, to protect your girl, because if you refuse, I will kill you, then kill your girl." I inwardly cursed when Carmine said this. I knew that as of this moment, I probably could beat them, but my promise to Alyssa would make me let them live…and give them an opportunity to kill me, and then they would go after Alyssa. I sighed in defeat, and began to pray to anything that my plan worked. I walked slowly towards Carmine, who held out the armlet with a smug looking face of victory. I was literally five feet away when my saving grace came.

"Oi, the Calvary is here!" Serenay yelled this as she drove up a natural ramp, flying over top of us. I took advantage of Carmine's distracted attention to knock the armlet two the ground, where Alyssa landed on it, breaking it in half.

"Layle, I'll take care of Carmine, you get Zane." I smiled and nodded when my girlfriend said this, who summoned her arm scythe blades and attacked Carmine. I turned and ran to Zane, who had started moving.

"Sorry mate, got to do this." I said this as I grabbed Zane by his shirt, and head-butted him. "Soul Calming." I said this as I projected myself into Zane's soul, leaving the fight to Alyssa and Serenay. It seemed like I was falling for a minute…that was till I hit the floor.

"Owww….that hurt." I said this as I picked myself up off the pure white floor. I stood in a white room with blue designs covering the walls. It had some comfy seats, and a set of empty shelves. And in one of the corners was a shadowy figure that resembled a small Omega Weapon.

"Who are you, and why are you here?" I turned to see Zane. He wore a white and blue suit. His face looked sad and lonely, like he was trapped. He simply sighed after he said this and walked over to a seat.

"My name is Layle. I'm here to help you Zane." I said this calmly, realizing that Zane had no memory of what had happened in the last two months, that or he just simply didn't care for my name. Zane just sighed. He turned his sight towards the shadow figure.

"Unless you can get rid of that thing… I am stuck here. So why do you even want to try…I can't beat it." Zane said this in a hopeless voice, but the look in his eye showed some ray of hope. I smiled and turned towards the shadow.

"A promise I made to your little sister. That's why I'm here, that's why I'm going to get you your body and soul back." I said this as I charged the shadow, connecting my fist with its chest. It skidded back as the Soul Room changed to encompass the battle. It roared and charged at me, its arms spread open to catch me. I easily jumped over it, changing my arms to Chaos's as I did so. I then charged the shadow myself and plunged my hand into its chest, crushing its essence when I grasped it. I changed my arms back as I dissolved and turned to Zane, who was dumbstruck.

"How do you know Alyssa?" Zane said this as he regained the ability to speak. I briefly smiled before walking towards him and holding my hand out.

"I'll fill you in later." I said this, and Zane and took my hand before whispering something useful into my ear, as his memory as an Omegian came back. I quickly brought us out of his Soul Room.

_~Alyssa~_

I charged Carmine as Layle head-butted my brother. I used my arm blades to attack Carmine, just so I could keep her occupied. Serenay was near Layle and Zane, ready to guard them.

"Layle was told to have no one follow him!" Carmine shrieked this as she slashed wildly at me. I parried her and counter slashed, scoring a hit on her shoulder. She jumped back as I followed up with a kick.

"I tagged along with Serenay when she said she was visiting her mother's grave." I said this simply as I jumped to avoid a sweeping kick Carmine did, and kicked her in the process. She flew back, her face now bruised and was about to charge me when Zane grabbed her shoulder, and Layle spoke something quickly in my mind.

"Carmine that is enough of this charade…it's over." Zane said this in a commanding voice that was so familiar to me. I smiled and deactivated my powers.

"Carmine, Zane has already told us that you're not affected by Omega's powers, and that you have only been playing the part so that you could protect Zane and me, though you did do a crummy job at the second part." Layle said this as he walked up to the little group with Serenay, who was quiet. Carmine's eyes widened and tears formed. She sank to her knees as she started sobbing.

"I'm so sorry…I just…had to try…that's why I was going to let Omega do the trade… So that Zane could get out…and Layle could…" Carmine said this through her sobs and Zane put a comforting arm around her.

"Carmine…thank you for trying. No one blames you for what you did…you just was trying to be convincing. So let's go." Layle said this as I realized that the blow that Layle took for me from Carmine, wouldn't have killed me… it only would have hit my shoulder. Carmine and Zane looked confused by what Layle had said.

"Go where?" Zane asked this and he and Carmine stood up. I smiled brightly and looked at Layle before looking at the two of them.

"The DWMA of course. Lord Death should welcome you guys quite nicely once we explain things."

**DE88: and there is chapter 4. Now review**

**Layle: Or you don't get cookies, and DE88 doesn't own shit, except for his own things.**


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